Step 1: The source data

  • Take a moment to look at how information about microarray experiments is annotated in this database. What information is recorded in this database? How is it organized?
  • Examine the Platform record. The term platform here refers to the microarray design itself. Explore the information that is annotated in the platform record.
  • Explore the structure of the Sample records. You can use the "View full table" button to get a view of all of the data. What is the structure of these records? What kinds of data does each contain?

Step 2: Look at the format of the table

  • There are two sections to these text files, a header and a data table. What information is held in each?
  • What do the rows of the data table represent?
  • What information about each row does each of the columns hold? Is there anything odd here?
  • What is the text format of this table? How are rows separated? How are elements within each row separated?
  • What is in the ID_REF column? Did you pick up the data in this column for your data.frame rownames when it was loaded? Why might this be good to do?
# Enter your code here!
head(ds.0)
##   CH1B_MEAN CH1B_MEDIAN CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2B_MEAN
## 1      2720        2608      7075      8925      7613      1424
## 2      2687        2600      7768      9300      7996      1381
## 3      2630        2584      4575      6168      4872      1327
## 4      2629        2568        64      1315        27      1340
## 5      2639        2568       662      1668       380      1345
## 6      2628        2576       481      1650       362      1334
##   CH2B_MEDIAN CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN  CORR FLAG  VALUE
## 1        1312         1367       7930       9297 0.000    0  0.165
## 2        1304         1358       8330       9688 0.000    0  0.101
## 3        1296         1350       5075       6425 0.000    0  0.150
## 4        1288         1342         28       1370 0.151    0 -1.193
## 5        1288         1342        396       1738 0.927    0 -0.741
## 6        1288         1342        377       1719 0.914    0 -0.351
##   PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH2I_1SD RAT1_MEAN RAT1N_MEAN
## 1           1.090             27             36     0.929      0.892
## 2           0.986             31             36     0.971      0.933
## 3           1.047             27             31     0.939      0.901
## 4           1.000              0              0     2.370      2.286
## 5           0.605             17             18     1.742      1.672
## 6           0.818              7             11     1.329      1.276
##   RAT2_MEAN RAT2N_MEAN  REGR TOT_BPIX TOT_SPIX TOP BOT LEFT RIGHT
## 1     1.076      1.121 0.000     1254       80  21  31   50    60
## 2     1.029      1.072 0.000     1074       80  21  31   61    71
## 3     1.065      1.109 0.000     1030       80  21  31   72    82
## 4     0.422      0.438 0.144     1030       80  21  31   83    93
## 5     0.574      0.598 0.598     1030       80  21  31   94   104
## 6     0.753      0.784 0.637     1030       80  21  31  105   115
##   UNF_VALUE
## 1     0.165
## 2     0.101
## 3     0.150
## 4    -1.193
## 5    -0.741
## 6    -0.351
summary(ds.0)
##    CH1B_MEAN     CH1B_MEDIAN     CH1D_MEAN       CH2I_MEAN    
##  Min.   :1580   Min.   :1560   Min.   :    1   Min.   :  803  
##  1st Qu.:2088   1st Qu.:2064   1st Qu.: 1406   1st Qu.: 2430  
##  Median :2385   Median :2328   Median : 2325   Median : 3456  
##  Mean   :2434   Mean   :2317   Mean   : 3925   Mean   : 5184  
##  3rd Qu.:2713   3rd Qu.:2568   3rd Qu.: 4266   3rd Qu.: 5557  
##  Max.   :7582   Max.   :3304   Max.   :51968   Max.   :55149  
##                                NA's   :47                     
##    CH2D_MEAN       CH2B_MEAN     CH2B_MEDIAN    CH2BN_MEDIAN 
##  Min.   :    3   Min.   : 826   Min.   : 816   Min.   : 850  
##  1st Qu.: 1240   1st Qu.:1144   1st Qu.:1112   1st Qu.:1158  
##  Median : 2250   Median :1313   Median :1248   Median :1300  
##  Mean   : 3986   Mean   :1350   Mean   :1220   Mean   :1271  
##  3rd Qu.: 4324   3rd Qu.:1467   3rd Qu.:1328   3rd Qu.:1383  
##  Max.   :53893   Max.   :6512   Max.   :1976   Max.   :2058  
##  NA's   :35                                                  
##    CH2DN_MEAN      CH2IN_MEAN         CORR              FLAG          
##  Min.   :    3   Min.   :  836   Min.   :-1.9870   Min.   :-100.0000  
##  1st Qu.: 1292   1st Qu.: 2531   1st Qu.: 0.0000   1st Qu.:   0.0000  
##  Median : 2344   Median : 3600   Median : 0.9280   Median :   0.0000  
##  Mean   : 4152   Mean   : 5400   Mean   : 0.6623   Mean   :  -0.3594  
##  3rd Qu.: 4505   3rd Qu.: 5789   3rd Qu.: 0.9610   3rd Qu.:   0.0000  
##  Max.   :56139   Max.   :57447   Max.   : 3.1840   Max.   :   0.0000  
##  NA's   :35                                                           
##      VALUE          PIX_RAT2_MEDIAN  PERGTBCH1I_1SD   PERGTBCH2I_1SD  
##  Min.   :-2.88300   Min.   :0.2140   Min.   :  0.00   Min.   :  0.00  
##  1st Qu.:-0.16800   1st Qu.:0.8510   1st Qu.: 35.00   1st Qu.: 37.00  
##  Median :-0.00100   Median :0.9570   Median : 48.00   Median : 53.00  
##  Mean   :-0.03209   Mean   :0.9498   Mean   : 51.17   Mean   : 55.48  
##  3rd Qu.: 0.14600   3rd Qu.:1.0500   3rd Qu.: 68.00   3rd Qu.: 75.00  
##  Max.   : 4.85800   Max.   :2.0000   Max.   :100.00   Max.   :100.00  
##  NA's   :71                                                           
##    RAT1_MEAN       RAT1N_MEAN      RAT2_MEAN         RAT2N_MEAN    
##  Min.   :0.036   Min.   :0.034   Min.   : 0.1280   Min.   : 0.136  
##  1st Qu.:0.941   1st Qu.:0.903   1st Qu.: 0.8550   1st Qu.: 0.890  
##  Median :1.042   Median :1.000   Median : 0.9600   Median : 1.000  
##  Mean   :1.091   Mean   :1.047   Mean   : 0.9651   Mean   : 1.005  
##  3rd Qu.:1.170   3rd Qu.:1.123   3rd Qu.: 1.0630   3rd Qu.: 1.107  
##  Max.   :7.800   Max.   :7.378   Max.   :28.0000   Max.   :29.000  
##  NA's   :50      NA's   :50      NA's   :50        NA's   :50      
##       REGR            TOT_BPIX         TOT_SPIX       TOP       
##  Min.   :-1.6740   Min.   : 595.0   Min.   :80   Min.   : 21.0  
##  1st Qu.: 0.0000   1st Qu.: 661.0   1st Qu.:80   1st Qu.:241.2  
##  Median : 0.7855   Median : 669.0   Median :80   Median :463.0  
##  Mean   : 0.6152   Mean   : 696.3   Mean   :80   Mean   :462.9  
##  3rd Qu.: 0.9310   3rd Qu.: 702.0   3rd Qu.:80   3rd Qu.:685.2  
##  Max.   : 4.8780   Max.   :1295.0   Max.   :80   Max.   :906.0  
##                                                                 
##       BOT             LEFT           RIGHT         UNF_VALUE      
##  Min.   : 31.0   Min.   : 49.0   Min.   : 59.0   Min.   :-2.8830  
##  1st Qu.:251.2   1st Qu.:269.2   1st Qu.:279.2   1st Qu.:-0.1670  
##  Median :473.0   Median :491.5   Median :501.5   Median : 0.0000  
##  Mean   :472.9   Mean   :492.2   Mean   :502.2   Mean   :-0.0310  
##  3rd Qu.:695.2   3rd Qu.:716.0   3rd Qu.:726.0   3rd Qu.: 0.1467  
##  Max.   :916.0   Max.   :936.0   Max.   :946.0   Max.   : 4.8580  
##                                                  NA's   :50

Step 3: Calculating a ratio

Step 4: Distribution of ratio values

How do the ratios compare if you use _MEDIAN pixel intensities instead of _MEAN intensities?

Step 5: Distribution of ratio values, Part 2